The Human Proteome Organization Brain Proteome Project (BPP) is using key features of Bruker Daltonics' ProteinScape database system for proteomics project management.
At the Human Proteome Organization (HUPO) 4th Annual World Congress, Bruker Daltonics announced that the HUPO Brain Proteome Project (BPP) Bioinformatics Committee has decided to include key features of its ProteinScape database system for proteomics project management in HUPO BPP's standard data reprocessing guidelines.
These capabilities include the ScoreBooster, Metascore and ProteinExtractor, which together are expected to further improve the quality and validation of information and knowledge gained from proteomics projects.
ProteinScape generates information using optimisation and validation strategies in every step in the mass spectrometry (MS) data interpretation process.
Peptide mass fingerprint (PMF) spectra are pre-processed with ScoreBooster, an algorithm that combines the steps of data calibration, removing calibrant signals and protein searches in an iterative manner, resulting in significant improvement of the protein identification rate.
ProteinScape integrates several different search engines including Mascot, Phenyx and Profound.
This allows cross-validation and consolidation of the identification results through the complementary use of several search engines using the novel MetaScore algorithm to provide enhanced reliability and to increase confidence by intelligent combination of scoring schemes from these different search engines.
The evaluation of proteins based on the peptides identified by these search engines is performed by the ProteinExtractor algorithm which generates true non-redundant protein lists from LC-MS/MS search results.
ProteinExtractor decreases redundancies in the protein results, reducing manual validation efforts significantly, says the company.
"These are the key features for our automated approach in analyzing the HUPO BPP pilot study data," stated Dr Christian Stephan of the BPP Bioinformatics Committee, who conducts brain proteomics research at the Ruhr University Medical Proteomics Center.
The aim of HUPO's BPP pilot studies is to derive in-depth knowledge from samples that are analyzed in laboratories worldwide using different separation and MS techniques.
The HUPO BPP data were collected, stored and submitted to ProteinScape, the chosen database system for project management.
Importantly, ProteinScape remains compliant with all applicable HUPO Proteomics Standards Initiative (PSI) standards.
To produce reliable, reproducible and comparable results, reprocessing of all proteomics data is currently performed with ProteinScape at the Data Collection Center in Bochum, Germany, in collaboration with the European Bioinformatics Institute in Hinxton, UK, and other collaborators.
Professor Helmut E.
Meyer, director of the HUPO Brain Proteome Project, pointed out: "In particular, the new features of ProteinScape allow us to store, handle and analyze the huge amount of data in a very effective way".
With Bruker Daltonics' addition of the mzData standard format to ProteinScape, mass spectrometry data comparison, exchange and verification have been facilitated.
The mzData format was established as a standard data exchange format by the HUPO PSI.
Research scientists get extraordinary flexibility in sharing these data more easily, greatly accelerating the process of extracting knowledge from the experimental data.
"The use of a sophisticated bioinformatics database system is a requirement for the successful management of the vast amount of heterogeneous data resulting from the great variety of workflow approaches used in proteomics today," said Professor Herbert Thiele, director of Bioinformatics at Bruker Daltonics.
"The HUPO BPP reprocessing effort clearly indicates the need for advanced algorithms for data evaluation and validation".
"More quality results generate more confidence and produce much more relevant knowledge".
